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Classification of autochthonous dengue virus type 1 strains circulating in Japan in 2014

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      Abstract

      In this paper, we classify by representativeness the elements of a set of complete genomic sequences of Dengue Virus Type 1 (DENV-1), corresponding to the outbreak in Japan during 2014. The set is coming from four regions: Chiba, Hyogo, Shizuoka and Tokyo. We consider this set as composed of independent samples coming from Markovian processes of finite order and finite alphabet. Under the assumption of the existence of a law that prevails in at least 50% of the samples of the set, we identify the sequences governed by the predominant law (see [ 1, 2]). The rule of classification is based on a local metric between samples, which tends to zero when we compare sequences of identical law and tends to infinity when comparing sequences with different laws. We found that the order of representativeness, from highest to lowest and according to the origin of the sequences is: Tokyo, Chiba, Hyogo, and Shizuoka. When comparing the Japanese sequences with their contemporaries from Asia, we find that the less representative sequence (from Shizuoka) is positioned in groups considerably far away from that which includes the sequences from the other regions in Japan, this offers evidence to suppose that the outbreak in Japan could be produced by more than one type of DENV-1.

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      Estimating the Dimension of a Model

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        Direct sequencing and characterization of a clinical isolate of Epstein-Barr virus from nasopharyngeal carcinoma tissue by using next-generation sequencing technology.

        Epstein-Barr virus (EBV)-encoded molecules have been detected in the tumor tissues of several cancers, including nasopharyngeal carcinoma (NPC), suggesting that EBV plays an important role in tumorigenesis. However, the nature of EBV with respect to genome width in vivo and whether EBV undergoes clonal expansion in the tumor tissues are still poorly understood. In this study, next-generation sequencing (NGS) was used to sequence DNA extracted directly from the tumor tissue of a patient with NPC. Apart from the human sequences, a clinically isolated EBV genome 164.7 kb in size was successfully assembled and named GD2 (GenBank accession number HQ020558). Sequence and phylogenetic analyses showed that GD2 was closely related to GD1, a previously assembled variant derived from a patient with NPC. GD2 contains the most prevalent EBV variants reported in Cantonese patients with NPC, suggesting that it might be the prevalent strain in this population. Furthermore, GD2 could be grouped into a single subtype according to common classification criteria and contains only 6 heterozygous point mutations, suggesting the monoclonal expansion of GD2 in NPC. This study represents the first genome-wide analysis of a clinical isolate of EBV directly extracted from NPC tissue. Our study reveals that NGS allows the characterization of genome-wide variations of EBV in clinical tumors and provides evidence of monoclonal expansion of EBV in vivo. The pipeline could also be applied to the study of other pathogen-related malignancies. With additional NGS studies of NPC, it might be possible to uncover the potential causative EBV variant involved in NPC.
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          Genomic sequence analysis of Epstein-Barr virus strain GD1 from a nasopharyngeal carcinoma patient.

          To date, the only entire Epstein-Barr virus (EBV) genomic sequence available in the database is the prototype B95.8, which was derived from an individual with infectious mononucleosis. A causative link between EBV and nasopharyngeal carcinoma (NPC), a disease with a distinctly high incidence in southern China, has been widely investigated. However, no full-length analysis of any substrain of EBV from this area has been reported. In this study, we analyzed the entire genomic sequence of an EBV strain from a patient with NPC in Guangdong, China. This EBV strain was termed GD1 (Guangdong strain 1), and the full-length sequence of GD1 was submitted to the GenBank database. The assigned accession number is AY961628. The entire GD1 sequence is 171,656 bp in length, with 59.5% G+C content and 40.5% A+T content. We detected many sequence variations in GD1 compared to prototypical strain B95.8, including 43 deletion sites, 44 insertion sites, and 1,413 point mutations. Furthermore, we evaluated the frequency of some of these GD1 mutations in Cantonese NPC patients and found them to be highly prevalent. These findings suggest that GD1 is highly representative of the EBV strains isolated from NPC patients in Guangdong, China, an area with the highest incidence of NPC in the world. Furthermore, these findings provide the second full-length sequence analysis of any EBV strain as well as the first full-length sequence analysis of an NPC-derived EBV strain.
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            Author and article information

            Affiliations
            [1 ] Department of Mathematics, Federal University of Technology, , Av. Monteiro Lobato, s/n – Km 04, Campus Ponta Grossa, Ponta Grossa, CEP 84016-210 Paraná, Brazil,
            [2 ] Department of Statistics, University of Campinas, , Sergio Buarque de Holanda, 651, Campinas, CEP 13083-859 São Paulo, Brazil,
            Author notes
            [* ]Corresponding author: marcoscordeiro@ 123456utfpr.edu.br
            Contributors
            Role: Guest Editor
            Journal
            fopen
            https://www.4open-sciences.org
            4open
            4open
            EDP Sciences
            2557-0250
            03 July 2019
            03 July 2019
            2019
            : 2
            : ( publisher-idID: fopen/2019/01 )
            10.1051/fopen/2019018 fopen190012
            © M.T.A. Cordeiro et al., Published by EDP Sciences, 2019

            This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

            Counts
            Figures: 3, Tables: 5, Equations: 43, References: 10, Pages: 8
            Product
            Self URI (journal page): https://www.4open-sciences.org/
            Categories
            Mathematics - Applied Mathematics
            Research Article
            Statistical Inference in Copula Models and Markov Processes, Case Studies and Insights
            Custom metadata
            4open 2019, 2, 20
            2019
            2019
            2019

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